An evo-devo geek's scientific meanderings

Month: February 2011

I get content alerts from a whole host of journals, some specialist publications focusing on my field, some more general. The majority of even the former is stuff I couldn’t care less about, and the ratio of interesting to irrelevant from generalist journals like PNAS or Nature is lower still. Nevertheless, sometimes you stumble on a title that isn’t directly related to your main interests, but still makes the whole rummaging through the Pile of Irrelevance worth it.

This was the case with a paper (Schirrmeister et al., 2011) just published in the online, open-access journal BMC Evolutionary Biology. It’s so fresh that they haven’t even formatted it – the full text is only available as a “provisional” pdf where all the figures are dumped at the back of the file, separated from their captions (why they can’t wait with publication until the damned thing is in readable format escapes me).

The study by Schirrmeister and others deals with an unusual group of bacteria. Cyanobacteria are probably still better known as blue-green algae, even though they have nothing to do with anything else we call an alga (well, in truth they have everything to do with algae, but in a rather more interesting way, as we’ll see below). If I had to pick one group of organisms that had the greatest impact on the history of our planet, cyanobacteria would be it. For more than two billion years, they have contributed huge amounts of biomass to the global carbon cycle. They are solely responsible for the oxygen-rich atmosphere of the earth – and, by extension, for most eukaryotic life and all animals. They are among the distinguished group of bacteria that can fix nitrogen – a vital ingredient of DNA and proteins – straight from the air, making it available for other organisms. Without them, the world would be a vastly different place, and we wouldn’t be possible. As Andrew Knoll puts it in his wonderful book Life on a Young Planet (consider this a recommendation ;)): “animals may be evolution’s icing, but bacteria are the cake”.

Cyanobacteria live everywhere there is light, from hot springs to the ocean to puddles to stone walls (as components of lichens). They also live inside the cells of every single eukaryote capable of photosynthesis: plants, red and green algae, brown algae, diatoms, dinoflagellates, euglenids (and any others I forgot to mention). The chloroplast is a pared down cyanobacterium – a symbiont that has lost most of its genes, but the ones that remain, together with its structure, still tell of its ancestry. Plants owe all their green splendour to these tiny buggers.

Cyanobacteria are not just immensely important, they are also quite unusual among prokaryotes. As the post title implies, they invented multicellularity. Multicellular cyanobacteria display a range of complexity. Some of them are just chains of identical cells. Others, though, have up to three different cell types. Heterocysts, thick-walled cells that ensure the oxygen-free environment that these bacteria require for nitrogen fixation, sit at regular intervals among “normal” cells, and when necessary, the “normal” cells can also differentiate into hardy resting cells that can survive bad times. The most complex cyanobacteria not only have filaments with different cell types, but also introduce branching into these filaments. This is the most complex prokaryotes get.

Filaments of an unbranched, differentiated cyanobacterium. The oversized heterocysts are quite obvious in some of them. Image by Kristian Peters, from Wikimedia Commons.

The new study raises an interesting possibility: that at least the simple form of multicellularity (i.e. undifferentiated filaments) occurred very early in the history of cyanobacteria. According to Schirrmeister et al., the vast majority of modern cyanobacteria descend from multicellular ancestors, even though a great many of them are single-celled today. Even more intriguingly, they find a lineage that might have re-evolved multicellularity after losing it. I don’t pretend to fully understand the methods used to come to these conclusions, but I have to say that it’s built on an impressive dataset – the group selected 58 cyanobacterial species for more detailed study from an original phylogenetic tree built from over a thousand taxa. They then constructed trees of this smaller dataset using two separate methods, and finally, tried to reconstruct the ancestral states at various points in those trees using several different statistical methods again. The analyses all agree: multicellularity is a very ancient trait in cyanobacteria, and it was lost left and right during their three-billion-year history.

These findings go against our ingrained view of evolution as an inexorable march towards increasing complexity. We, mammals, are among the (if not the) most complex organisms the earth has ever produced. We are assemblages of some 200 distinct cell types organised into a finely regulated machinery of a multitude of specialised organs. When we look at the large-scale patterns in the fossil record, we also see that this complexity has accumulated from much simpler beginnings over the aeons. We can be forgiven for thinking, in a characteristically self-centred way, that complexity is where evolution is intrinsically headed. But every now and then, nature reminds us that “more complicated” does not necessarily equal “favoured”.

Parasites are probably best known for their tendency to become simplified – after all, if you are bathed in your host’s digestion products all the time, why waste your energy on growing your own gut? However, simplification is abundant in organisms that make their own living, too. For example, two entire phyla of distinctly unsegmented, baglike worms – spoon worms and peanut worms -, likely came from more sophisticated segmented worms (Struck et al., 2007). Now, cyanobacteria join the club, and new questions surge in their wake. Why did they go back to unicellularity? How difficult is it for them to become multicellular? Such questions, of course, can be asked about any complex trait that followed a similar evolutionary trajectory.

Most intriguingly, these tiny microbes seem to violate another “law” of evolution, known as Dollo’s law: that once lost in a lineage, a complex trait won’t reappear. If the inferences of Schirrmeister et al. are correct, then either simple multicellularity isn’t such a big deal at all for these bacteria, or Dollo’s law isn’t as much of a law as we thought.

(Actually, the latter is probably the case however the history of cyanobacteria turns out. Dollo’s law has been questioned by others, and it was recently dealt a spectacular blow by a frog that almost certainly re-evolved teeth in its lower jaw (Wiens, 2011) after at least 200 million years of not having them.)

Evolution is a fascinating story. As the example of cyanobacterial multicellularity suggests, it can also be as complex as any good novel. I for one think this makes for a much more interesting and fulfilling narrative than simplistic listings of “what’s new” through the ages.

Wiens JJ (2011) Re-evolution of lost mandibular teeth in frogs after more than 200 million years, and re-evaluation of Dollo’s Law. Evolution advance online publication, DOI: 10.1111/j.1558-5646.2011.01221.x

I’m not technically new to the blogging enterprise. I’ve kept a private journal-and-repository-of-ideas for years now, but whenever I felt like I had something to say that was worth sharing, I inevitably changed my mind. But, with so much wonderful, exciting stuff out there, isn’t it practically a crime for a scientist not to share?

I thought it fitting to start my science blogging career with tetrapod limbs, since they played a great part in setting me on the path that led me where I am today. If I had to define my specialisation, I would call myself an evolutionary developmental geneticist. (Add “molecular” in there somewhere to make it more accurate and more cumbersome ;)) This means investigating the genes that control the formation of body parts in various organisms, and trying to figure out what this tells us about the evolution of said body parts. One of the early signs that alerted me to the awesomeness of the field was a paper about limbs (Davis et al., 2007) – more precisely, about how the genetic program that specifies our fingers and toes is present in the fins of fish with nothing resembling digits. That is an intriguing story that I might tell another day, but today, I will discuss something else to do with limbs, apropos a study that came out recently in Science.

Birds have some of the most extremely modified forelimbs among tetrapods. If you squint at the skeleton inside the wing hard enough, you may be able to recognise the stunted remains of three digits. The homology of those three digits to the digits of more conventional forelimbs has been a conundrum ever since someone first examined the limb buds of a bird embryo.

Homology is a tricky concept. It was originally defined before the theory of evolution took off, by a guy who had a rather strange relationship with Darwin and Wallace’s theory later on. Richard Owen (see here for a biography) defined homology as:

the same organ in different animals under every variety of form and function

Later, evolutionary biology embraced the word as a neat shorthand for structures, processes, genes, even behaviours, that evolved from a common ancestor. The obvious problem is that organs and genes don’t come with labels listing what they are homologous to. Therefore, homology has to be inferred. These inferences can be based on a variety of sources such as morphological similarity, fossil evidence, embryonic origin and shared genetic programs. The more lines of evidence converge on the same conclusion, the stronger the conclusion is. But what happens when those different sources contradict?

In the case of avian digits, morphology [1], and later palaeontology, suggested that they were digits I, II and III, that is, a thumb, an index and a middle finger. While it’s a bit hard to say anything about the morphology of those fused and stunted bones in a modern wing with a straight face, the fossil evidence is pretty unambiguous. As you go from the earliest dinosaurs to birds, you can clearly follow the loss of digit V first, followed by digit IV. The remaining three digits are quite clearly I-II-III in animals such as Archaeopteryx.

A comparison of the metacarpals (palms) of dinosaurs. Left to right, in order of increasing relatedness to birds: Herrerasaurus (note the vestigial fifth metacarpal (labelled "V")), Coelophysis (MCV gone), Allosaurus (MC4 gone), Deinonychus, Archaeopteryx, and Nothura (a modern tinamou). Image from Wagner and Gauthier (1999)

However, embryos seemed to tell a completely different story. During development, the skeleton of a limb forms from little condensations of tissue inside the limb bud (which, at that point, looks more like a weird-shaped sausage than a limb). These condensations are first cartilaginous, later laying down bone. Around the forming digits, muscles and connective tissues organise, and finally, the padding between the digits dies away, transforming the paddle-like limb bud into a hand or foot [2]. The forelimbs of birds make four condensations – more than needed to form their three digits, but fewer than five, making it difficult to tell exactly which ones remain.

Nevertheless, regularities observed in limb development gave scientists clues. The condensations that turn into digits in tetrapods don’t all form at the same time – in fact, they form in a stereotypical order in which CIV forms first and CI last (Burke and Feduccia, 1997). Condensation (and digit) IV is considered part of the main axis of the limb (the so-called metapterygial axis), and its presence is thought to be essential for the other condensations to form. You cannot lose CIV without losing all the rest, so conventional wisdom went. That means that birds must have a CIV. And indeed, the third digit of a wing comes from something that looks suspiciously like a CIV, with two other condensations appearing in front of it and one behind. Thus, embryology would have us think that the digits are II, III and IV.

Diagram comparing the development of the forelimb skeleton in alligators (top) and ostriches (bottom). Image from Wagner and Gauthier (1999).

This presents a dilemma that is a common one in evo-devo. Which kind of evidence do you put more stock in? Is there a way to resolve the conflict, or does it spell doom for the hypothesis that birds evolved from dinosaurs (and then, what’s up with the four- and three-fingered dinosaurs that obviously aren’t birds?)? What’s going on here?

An important paper (Wagner and Gauthier, 1999) over a decade ago suggested a possible resolution called the developmental frame shift hypothesis. They proposed that birds do in fact form condensations II-IV – but then something strange happens. The genetic program that specifies digit identity is not switched on until all pre-digital condensations have formed. Thus, a condensation can become any digit, depending on which genes are expressed at its location. So, Wagner and Gauthier said, at some point in their history, dinosaurs shifted the “normal” forelimb gene expression patterns backwards, so CII now ended up in the genetic environment of DI, and thus formed a DI. That is, the fingers of birds are homologous to different digits of the basic pentadactyl limb at different levels.

Over the years since, strong genetic support has been gathered for this idea. The first digit of the hand of a bird does, indeed, form in an area that bears the genetic hallmarks of DI in more typical tetrapods, including the closest living relatives of birds (Vargas et al., 2008). So, the frameshift hypothesis of Wagner and Gauthier seems to stand on pretty solid legs.

A recent study had a new look at wing development, confirming the identity of wing digits as I-III. Tamura and others (2011) followed the origin of digits at the cellular level. An early limb bud, before it has much obvious internal structure, already contains what developmental biologists call organisers or signalling centres. At the tip of the bud, a narrow ridge (the so-called apical ectodermal ridge, or AER) gives off chemical signals that direct the correct outgrowth of the limb. At the posterior, tailward side of the bud, there is an area called the Zone of Polarising Activity, which defines the anterior-posterior polarity of the limb: the side of the ZPA is the pinky side, and where everything else develops is determined by the levels of morphogens – most famously the protein Sonic hedgehog – that diffuse from the ZPA.

In ordinary, five-fingered tetrapods, the ZPA contributes tissue to the fifth and fourth condensations (and digits). The first thing Tamura and colleagues did, then, was to transplant ZPAs between the fore- and hindlimb buds of chick embryos (remember, chicken legs are four-toed). When you add a ZPA on the wrong side of a limb bud, you get a mirror image duplication of the limb. (How much is duplicated depends on the age of the transplant and the recipient.) In this study, the researchers found that a hindlimb ZPA of the right age grafted onto a forelimb bud often led to the formation of hindlimb digits in the forelimb. The converse was not true: the forelimb ZPA was almost invariably unable to form forelimb digits, though it was able to induce the doubling of the foot. Thus, it seems cells in the forelimb ZPA aren’t good at making digits on their own, only at directing other tissues to form digits.

The second experiment involved tracing cell lineages with a clever method that’s widely used in similar experiments due to its relative simplicity. They stained cells with a dye that sticks to the cell membrane. This dye is inherited by the descendants of the mother cell: when it divides, the daughter cells will split the original membrane – and the dye – between them. So, if the ZPA contributes to the last digit of the wing, we should see staining in the digit if we’d dyed the ZPA before digits begin to condense. In the foot, that’s exactly what happens. Not so in the wing: the last digit forms outside the ZPA, with no contribution from the labelled cells.

And lastly, the researchers went further back in time, using the same cell labelling method to trace the fate of different parts of the limb bud from an even earlier stage. What they found is that the region that gives rise to the third finger does lie inside the ZPA at this point – but it leaves the zone very soon after, unlike the progenitor of the fourth toe. Thus, well before any condensation is apparent, this bit of tissue is different from conventional fourth digits.

Interestingly, what this study identifies as a digit III based on its origin appears to lie on the metapterygial axis – a place thought to be the privilege of fourth digits. What’s more, removing the posterior portion of the limb bud relocates the second digit to the main axis. Thus, it appears that limb development is a lot more flexible than Burke and Feduccia had concluded over a decade earlier.

So, in a sense, Wagner and Gauthier were wrong – but in a different sense, they were more right than they thought. It appears that the frame shift they hypothesised doesn’t happen after condensations appear: it happens well before. What was previously identified as “CIV” already bears characteristics of CIII when the first lumps of cartilage begin to form.

In a way, the story of avian digits is a beautiful illustration of the scientific process. From a controversy sparked by a seemingly insurmountable contradiction, we have moved to a synthesis that accounts for all available evidence. Scientists did not dismiss the contradiction, they worked to make sense of it. They called on new lines of evidence to resolve what the old evidence could not. Some ideas proposed in the process – such as the rigidity of the digit developmental program – turned out largely wrong. Others – the original frame shift hypothesis – still seem somewhat wrong, but their essence carried over into the newest picture. It’s entirely possible that this isn’t the last word on bird fingers either. But at this point, I am reminded of Asimov’s essay The Relativity of Wrong (Asimov, 1989). Whatever the future brings, it’s a good bet that we’re not nearly as “wrong” as we were before.

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[1] Comparing ordinary, five-fingered forelimbs, some characteristics are pretty consistent across the different groups of tetrapods. Most importantly, thumbs have only two phalanges, fewer than all the other digits.

[2] This isn’t universally the case. When the interdigital tissue doesn’t disappear, you get webbed feet.

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References:

Asimov I (1989) The Relativity of Wrong. The Skeptical Inquirer14:35-44

Burke AC and Feduccia A (1997) Developmental patterns and the identification of homologies in the avian hand. Science278:666-668

Davis MC, Dahn RD and Shubin NH (2007) An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature447:473-476